Related papers: Tropical Density Estimation of Phylogenetic Trees

Learning informative representations of phylogenetic tree structures is essential for analyzing evolutionary relationships. Classical distance-based methods have been widely used to project phylogenetic trees into Euclidean space, but they…

There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…

Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…

Tree shape statistics provide valuable quantitative insights into evolutionary mechanisms underpinning phylogenetic trees, a commonly used graph representation of evolution systems ranging from viruses to species. By developing limit…

The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…

As an alternative to parsimony analyses, stochastic models have been proposed (Lewis, 2001), (Nylander, et al., 2004) for morphological characters, so that maximum likelihood or Bayesian analyses may be used for phylogenetic inference. A…

The reconstruction of a species tree from genomic data faces a double hurdle. First, the (gene) tree describing the evolution of each gene may differ from the species tree, for instance, due to incomplete lineage sorting. Second, the…

Measuring the complexity of tree structures can be beneficial in areas that use tree data structures for storage, communication, and processing purposes. This complexity can then be used to compress tree data structures to their…

'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…

Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from…

We investigate the tree gonality of a genus-$g$ metric graph, defined as the minimum degree of a tropical morphism from any tropical modification of the metric graph to a metric tree. We give a combinatorial constructive proof that this…

It was recently observed by de Vienne et al. that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on…

Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…

Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…

Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…

Species richness varies widely across the tree of life, and there is great interest in identifying ecological, geographic, and other factors that affect rates of species proliferation. Recent methods for explicitly modeling the…

Hilbertian kernel methods and their positive semidefinite kernels have been extensively used in various fields of applied mathematics and machine learning, owing to their several equivalent characterizations. We here unveil an analogy with…

Bayesian phylogenetics is vital for understanding evolutionary dynamics, and requires accurate and efficient approximation of posterior distributions over trees. In this work, we develop a variational Bayesian approach for ultrametric…

We present a new class of metrics for unrooted phylogenetic $X$-trees derived from the Gromov-Hausdorff distance for (compact) metric spaces. These metrics can be efficiently computed by linear or quadratic programming. They are robust…

In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species…